Difference between revisions of "Model Overview"
(→Parameters for model reactions) |
(→Parameters for model reactions) |
||
Line 223: | Line 223: | ||
|0.11−5.65 | |0.11−5.65 | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | |0. | + | |0.572 |
− | | | + | |3.5 |
− | |0. | + | |0.2514 |
− | |0. | + | |0.89956 |
|- | |- | ||
|<math>k_{onA}</math> | |<math>k_{onA}</math> | ||
Line 232: | Line 232: | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
|0.587 | |0.587 | ||
− | | | + | |3.875 |
− | |0. | + | |0.35255 |
− | | | + | |0.94054 |
|- | |- | ||
|rowspan="2" |[[Antisense interaction between r and a]] | |rowspan="2" |[[Antisense interaction between r and a]] | ||
Line 241: | Line 241: | ||
|<math> nM </math> | |<math> nM </math> | ||
|7.8 | |7.8 | ||
− | | | + | |7.27 |
− | |3. | + | |3.4665 |
− | |1. | + | |1.1882 |
|- | |- | ||
|<math>k^{-}_{ar}</math> | |<math>k^{-}_{ar}</math> | ||
|0.006−6 | |0.006−6 | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | |0. | + | |0.223 |
− | | | + | |4.8 |
− | |−0. | + | |−0.43359 |
− | |1. | + | |1.0326 |
|- | |- | ||
|[[Translation of R]] | |[[Translation of R]] | ||
Line 257: | Line 257: | ||
|0.165−5.86 | |0.165−5.86 | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | |0. | + | |0.744 |
− | | | + | |3.2 |
− | |0. | + | |0.42952 |
− | |0. | + | |0.85176 |
|- | |- | ||
|[[Translation of A]] | |[[Translation of A]] | ||
Line 266: | Line 266: | ||
|0.11−4 | |0.11−4 | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | |0. | + | |0.5 |
− | | | + | |3.2 |
− | |0. | + | |0.053356 |
− | |0. | + | |0.85327 |
|- | |- | ||
|rowspan="2" |[[Formation of homo-dimer R2 |Formation of homo-dimer R<sub>2</sub>]] | |rowspan="2" |[[Formation of homo-dimer R2 |Formation of homo-dimer R<sub>2</sub>]] | ||
Line 275: | Line 275: | ||
|2.58-42.9 | |2.58-42.9 | ||
|<math> nM </math> | |<math> nM </math> | ||
− | | | + | |3.89 |
− | | | + | |1.9 |
− | | | + | |1.6716 |
− | | | + | |0.55779 |
|- | |- | ||
|<math>k^{-}_{6}</math> | |<math>k^{-}_{6}</math> | ||
|0.144-51.2 | |0.144-51.2 | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | | | + | |N/A |
− | | | + | |N/A |
− | |2. | + | |2.5303 |
− | |1. | + | |1.5324 |
|- | |- | ||
|[[Degradation of r]] | |[[Degradation of r]] | ||
Line 293: | Line 293: | ||
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
|0.14 | |0.14 | ||
− | | | + | |2.06 |
− | |−1. | + | |−1.5916 |
− | |0. | + | |0.60824 |
|- | |- | ||
|[[Degradation of R]] | |[[Degradation of R]] | ||
|<math>d_{R}</math> | |<math>d_{R}</math> | ||
− | |<math> | + | |<math>5.02 \cdot 10^{-4}- 0.00578</math> |
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | |<math>0. | + | |<math>0.00144</math> |
− | | | + | |1.78 |
− | |−6. | + | |−6.2837 |
− | |0. | + | |0.50981 |
|- | |- | ||
|[[Degradation of R2 |Degradation of R<sub>2</sub>]] | |[[Degradation of R2 |Degradation of R<sub>2</sub>]] | ||
|<math>d_{R_{2}}</math> | |<math>d_{R_{2}}</math> | ||
− | |<math> | + | |<math>5.02 \cdot 10^{-4}- 0.00578</math> |
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | |<math>0. | + | |<math>0.00144</math> |
− | | | + | |1.78 |
− | |−6. | + | |−6.2837 |
− | |0. | + | |0.50981 |
|- | |- | ||
|[[Degradation of a]] | |[[Degradation of a]] | ||
Line 320: | Line 320: | ||
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
|0.14 | |0.14 | ||
− | | | + | |2.06 |
− | |−1. | + | |−1.5916 |
− | |0. | + | |0.60824 |
|- | |- | ||
|[[Degradation of A]] | |[[Degradation of A]] | ||
|<math>d_{A}</math> | |<math>d_{A}</math> | ||
− | |<math> | + | |<math>5.02 \cdot 10^{-4}- 0.00578</math> |
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | |<math>0. | + | |<math>0.00144</math> |
− | | | + | |1.78 |
− | |−6. | + | |−6.2837 |
− | |0. | + | |0.50981 |
|- | |- | ||
|[[Degradation of C]] | |[[Degradation of C]] | ||
Line 337: | Line 337: | ||
|<math>7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}</math> | |<math>7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}</math> | ||
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | |<math>0. | + | |<math>0.0032</math> |
− | | | + | |5.1 |
− | |−4. | + | |−4.6234 |
− | |1. | + | |1.0539 |
|- | |- | ||
|[[Degradation of C2-R2 |Degradation of C<sub>2</sub>-R<sub>2</sub>]] | |[[Degradation of C2-R2 |Degradation of C<sub>2</sub>-R<sub>2</sub>]] | ||
|<math>d_{CR}</math> | |<math>d_{CR}</math> | ||
− | |<math> | + | |<math>5.02 \cdot 10^{-4}- 0.00578</math> |
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | |<math>0. | + | |<math>0.00144</math> |
− | | | + | |1.78 |
− | |−6. | + | |−6.2837 |
− | |0. | + | |0.50981 |
|- | |- | ||
|[[Degradation of A-R2 |Degradation of A-R<sub>2</sub>]] | |[[Degradation of A-R2 |Degradation of A-R<sub>2</sub>]] | ||
|<math>d_{AR}</math> | |<math>d_{AR}</math> | ||
− | |<math> | + | |<math>5.02 \cdot 10^{-4}- 0.00578</math> |
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | |<math>0. | + | |<math>0.00144</math> |
− | | | + | |1.78 |
− | |−6. | + | |−6.2837 |
− | |0. | + | |0.50981 |
|- | |- | ||
|[[Degradation of r-a]] | |[[Degradation of r-a]] | ||
Line 364: | Line 364: | ||
|0.35−69.3 | |0.35−69.3 | ||
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | | | + | |4.9 |
− | | | + | |14.1 |
− | |2. | + | |2.5669 |
− | | | + | |0.98835 |
|- | |- | ||
|[[Diffusion of C and Ce |Diffusion of C and C<sub>e</sub>]] | |[[Diffusion of C and Ce |Diffusion of C and C<sub>e</sub>]] | ||
Line 374: | Line 374: | ||
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
|2.8 | |2.8 | ||
− | | | + | |4.27 |
− | | | + | |1.9947 |
− | | | + | |0.98233 |
|- | |- | ||
|[[Degradation of Ce]] | |[[Degradation of Ce]] | ||
− | |||
|<math>7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}</math> | |<math>7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}</math> | ||
|<math>min^{-1}</math> | |<math>min^{-1}</math> | ||
− | |<math>0. | + | |<math>0.0032</math> |
− | | | + | |5.1 |
− | |−4. | + | |−4.6234 |
− | |1. | + | |1.0539 |
|- | |- | ||
|[[Cellular growth]] | |[[Cellular growth]] |
Revision as of 17:41, 23 November 2017
Contents
List of Model Reactions
*1 Reactions taking place only in the scenario which includes the activating complex
*2 Reactions taking place only in the scenario which includes the antisense RNA interactions
Reactions |
---|
*1
*1 *1 *1 *1 *1
*1 *2
*1 *2
|
Parameters for model reactions
Reaction | Parameter | Value | Units | Distribution
Mode |
Spread | Location
parameter (μ) |
Scale
parameter (σ) |
---|---|---|---|---|---|---|---|
Binding of R2 to OR operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Binding of R2 to OA operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Binding of R2 to A | 10.02 | 13.192 | 1.2977 | ||||
N/A | N/A | 9.9423 | 1.5503 | ||||
Binding of R2 to C | N/A | N/A | 5.9389 | 2.3412 | |||
0.816 | 244 | 4.2872 | 2.119 | ||||
Binding of A-R2 to OA' operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Synthesis of C | 0.00315−85.5 | 0.094 | 60.49 | 0.87914 | 1.8017 | ||
Transcription of r | 0.16−8.24 | 0.8346 | 3.55 | 0.63056 | 0.90076 | ||
18.2−33 | 20.7 | 1.34 | 3.1107 | 0.28276 | |||
0.0518-14.5 | 0.867 | 4.09 | 0.78694 | 0.96428 | |||
Transcription of a | 0.001−0.2 | 0.0037 | 10.93 | −3.8324 | 1.3259 | ||
0.11−5.65 | 0.572 | 3.5 | 0.2514 | 0.89956 | |||
0.039-8.82 | 0.587 | 3.875 | 0.35255 | 0.94054 | |||
Antisense interaction between r and a | 0.4−89 | 7.8 | 7.27 | 3.4665 | 1.1882 | ||
0.006−6 | 0.223 | 4.8 | −0.43359 | 1.0326 | |||
Translation of R | 0.165−5.86 | 0.744 | 3.2 | 0.42952 | 0.85176 | ||
Translation of A | 0.11−4 | 0.5 | 3.2 | 0.053356 | 0.85327 | ||
Formation of homo-dimer R2 | 2.58-42.9 | 3.89 | 1.9 | 1.6716 | 0.55779 | ||
0.144-51.2 | N/A | N/A | 2.5303 | 1.5324 | |||
Degradation of r | 0.03−0.365 | 0.14 | 2.06 | −1.5916 | 0.60824 | ||
Degradation of R | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of R2 | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of a | 0.03−0.365 | 0.14 | 2.06 | −1.5916 | 0.60824 | ||
Degradation of A | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of C | 5.1 | −4.6234 | 1.0539 | ||||
Degradation of C2-R2 | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of A-R2 | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of r-a | 0.35−69.3 | 4.9 | 14.1 | 2.5669 | 0.98835 | ||
Diffusion of C and Ce | 0.1−24 | 2.8 | 4.27 | 1.9947 | 0.98233 | ||
Degradation of Ce | 5.1 | −4.6234 | 1.0539 | ||||
Cellular growth | Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): μ | 0.0004−0.0107 | 0.0022 | 7.5 | −5.4517 | 0.80808 |
Parameters for cell colony growth
Parameter | Value | Units |
---|---|---|
Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): τ | ||
Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): λ | ||
Initial concentrations of species
Species | Initial concentration | Units | Compartment |
---|---|---|---|
OR | 0.9592 | Cell | |
OA | 0.9592 | Cell | |
OR-R2 | 0 | Cell | |
OA-R2 | 0 | Cell | |
OA'-AR2 | 0 | Cell | |
r | 0 | Cell | |
a | 0 | Cell | |
r-a | 0 | Cell | |
R | 0 | Cell | |
R2 | 0 | Cell | |
A | 0 | Cell | |
C | 0 | Cell | |
AR2 | 0 | Cell | |
C2R2 | 0 | Cell | |
Ce | 0 | Environment |